[gmx-users] Problem regarding Complex ion addition by genbox

[chris.neale at utoronto.ca]

> Thanks for giving me insight. But i have a query.
> I tried to add complex ion by genion but while adding, it replaces the
> water molecule according to my choice but it shows information of one atom
> only not of all atom of that complex molecule in structure file (.gro).i
> then tried to use by genbox.How should it will display information of all
> atom of complex molecule ?

I'll do my best to answer, but if you want some better help then I am  
afraid that you need to find somebody on your end that can assist you  
in getting the question across in english that is more easily  
understood. Unfortunately I do not understand your particular question  
on this post, I only assume that you still don't have the answer.

Here is what I would first think of doing (but I have never tried it).

1. Use editconf to put your protein in the box of desired size (protein.gro).

2. Use editconf to put your guanidinium ion in a box of such a size so  
that it is at the desired concentration (guanidinium.gro).

3. genbox -cp protein.gro -cs guanidinium.gro -o protein_guanidinium.gro

4. grnbox -cp protein_guanidinium.gro -cs tip3p.gro -o  
protein_guanidinium_tip3p.gro

5. EM

6. Posre ME

7. MD

Hope it helps,
Chris.

>> I tried with genbox option with perticular concentration i.e.
>> perticular
>> number of each component like guanidium ion thiocynate ion & water
>> molecule.But while doing PR(position restrain MD) it showing errors :
>> constraints errors in algorithm shake at step 0. t=o.oo ps : water
>> molecule starting at atom 3010 can not be settled. check for bad
>> contacts
>> and/or reduce the time steps.
>
> Quote from 'genion -h',
> "For larger ions, e.g. sulfate we recommended to use genbox."
>
> If you must use genion for some reason then the only question I see is:
> Did you do EM? If not then try that first. Also, for genion or genbox,
> you might try simplifying your system. Take a box of water and use
> genion to add a single guanidium. Then EM, then MD (dt=0.002). What
> happens?
>
> Chris.
>
>> i reduced the time steps in pr.mdp from .002 to .001 ps file but again
>> it
>> shows the same problem. i have seen the pdb files after genbox really
>> some
>> close contacts between was there it means insertion of extra molecule by
>> gen box is not proper it leads to some bad contacts.
>>
>> The real problem is that when performing simulation of peptide with
>> guanidium ion , CL- , water it is showing no problem because CL- is
>> added
>> in genion steps. Only change in new system (guanidium ion, SCN- , water,
>> peptide) is of SCN-. Addition of SCN- in genbox step is creating
>> problem.
>> Is any other method to  perform simulation of peptide in solvent systrm
>> (guanidium ion, SCN-, water).
>> Please give me some insight to resolve this issue.
>> This is pr.mdp file
>>
>> title               =  Nanomer                  ; a string
>> cpp                 =  /lib/cpp                 ; c-preprocessor
>> define              =  -DPOSRES
>> dt                  =  0.001                    ; time step
>> integrator          =  md
>> tinit               =  0.0
>> nsteps              =  100000                   ; number of steps
>> nstcomm             =  1                        ; reset c.o.m. motion
>> nstxout             =  500                      ; write coords
>> nstvout             =  500                      ; write velocities
>> nstfout             =  0
>> nstlog              =  500                      ; print to logfile
>> nstenergy           =  500                      ; print energies
>> nstlist             =  10                       ; update pairlist
>> ; Neighbour Searching
>> ns_type             =  grid                     ; pairlist method
>> ; Electrostatics and VdW
>> coulombtype         =  PME
>> vdwtype             =  shift
>> rlist               =  1.5                      ; cut-off for ns
>> rvdw_switch         =  0.8
>> rvdw                =  1.4                      ; cut-off for vdw
>> rcoulomb_switch     =  0.8
>> rcoulomb            =  1.5                      ; cut-off for coulomb
>> ;Temperature coupling
>> Tcoupl              =  berendsen                ; temperature bath
>> (yes,no)
>> ref_t               =  298 298
>> tc-grps             =  Protein Non-Protein
>> tau_t               =  0.1 0.1
>> ; Pressure coupling
>> Pcoupl              =  no                       ; pressure bath
>> tau_p               =  0.5
>> compressibility     =  4.5e-5
>> ref_p               =  1.0
>> ; Velocity generation
>> gen_vel             =  yes                      ; generate initial
>> gen_temp            =  298.0                    ; initial temperature
>> gen_seed            =  173529                   ; random seed
>> constraints         =  all-bonds
>> constraint_algorithm      =  shake
>> shake_tol           = 0.0001
>
>
>
>
>> kinshuk at chem.iitb.ac.in wrote:
>>> Hi all,
>>>
>>>   I have been trying to simulate peptide in water box with guanidium
>>> ion
>>> &
>>> thiocynate ion(SCN-).I tried to add these ion by genion command line by
>>> simply adding topology information of these ion in ions.itp of gromacs
>>> library directory but it is not working properly it only adds one atom
>>> by replacing water molecule it seems that genion is applicable only for
>>> monoatomic ion.
>>>   If i have to do simulation with these polyatomic ions with perticular
>>> salt concentration how do i will perform it.
>>>
>> with genbox. compute number yourself.
>>>
>>> Kinshuk
>>> IIT-Bombay
>>> India